Variant report

Variant	rs7047636
Chromosome Location	chr9:102579467-102579468
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:102579378-102579523	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:102579454..102582118-chr9:102626994..102629896,2	K562	blood:
2	chr9:102574602..102579985-chr9:102580747..102585287,6	MCF-7	breast:
3	chr9:102568705..102572771-chr9:102577522..102579718,3	MCF-7	breast:

Variant related genes	Relation type
NR4A3	TF binding region
ENSG00000237461	Chromatin interaction
ENSG00000119508	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10156557	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988895	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10988898	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988904	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988905	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336436	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1405209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417738	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16918734	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918008	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918009	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965564	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900222	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742773	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742774	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019989	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022059	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029504	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029559	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038780	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041475	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744685	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893621	chr9:102342950-102585545	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv528025	chr9:102540386-102613672	Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv893622	chr9:102543355-102595685	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7047636	PPP3R2	cis	cerebellum	SCAN
rs7047636	C9orf125	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102557400-102581400	Weak transcription	Pancreas	Pancrea
2	chr9:102559800-102581600	Weak transcription	Gastric	stomach
3	chr9:102560000-102580600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:102560400-102580800	Weak transcription	Fetal Stomach	stomach
5	chr9:102561200-102580800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:102562800-102580800	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:102562800-102580800	Weak transcription	HSMMtube	muscle
8	chr9:102564400-102580000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:102564400-102581400	Weak transcription	Ovary	ovary
10	chr9:102566000-102580800	Weak transcription	Left Ventricle	heart
11	chr9:102566600-102580800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr9:102567400-102581600	Weak transcription	Lung	lung
13	chr9:102570000-102580600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:102570000-102580800	Weak transcription	Liver	Liver
15	chr9:102570400-102580800	Weak transcription	Fetal Brain Female	brain
16	chr9:102570600-102579800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:102570600-102580600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:102570600-102580800	Weak transcription	Osteobl	bone
19	chr9:102570800-102580800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:102571200-102580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:102572600-102580600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:102572600-102580800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:102573200-102580600	Weak transcription	Brain Hippocampus Middle	brain
24	chr9:102573600-102580600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:102573600-102580800	Weak transcription	HMEC	breast
26	chr9:102573600-102581600	Weak transcription	Spleen	Spleen
27	chr9:102573800-102580600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:102573800-102580800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:102573800-102580800	Weak transcription	Hela-S3	cervix
30	chr9:102574200-102580200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:102574200-102580600	Weak transcription	Primary B cells from cord blood	blood
32	chr9:102574200-102580800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:102574200-102581000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:102574200-102581400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr9:102574200-102581400	Weak transcription	Aorta	Aorta
36	chr9:102574400-102580800	Weak transcription	Placenta	Placenta
37	chr9:102574800-102580800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:102576200-102580800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr9:102576200-102580800	Weak transcription	Right Ventricle	heart
40	chr9:102576400-102580800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr9:102577400-102580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr9:102577600-102580400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr9:102577600-102580600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr9:102577600-102580800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr9:102577600-102580800	Weak transcription	Brain Substantia Nigra	brain
46	chr9:102577800-102580600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:102577800-102580600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr9:102577800-102580800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr9:102577800-102580800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr9:102577800-102580800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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